Abstract
RNA viruses evolve rapidly, enabling them to evade host immunity and antiviral therapies and complicating durable diagnostics strategies. There is a pressing need for approaches that provide broad-spectrum viral suppression and detection. We designed four Cas13d crRNAs targeting a conserved 26-nucleotide sequence in coronavirus (CoV) nsp12. Their antiviral efficacy was evaluated in vitro against the target sequences of all seven human CoVs, showing potent activity across the tested samples. The same crRNAs were adapted for a Cas13d-based specific high-sensitivity enzymatic reporter unlocking (SHERLOCK) assay to detect multiple human CoVs, demonstrating high sensitivity, with the ability to detect as few as a single copy of SARS-CoV-2 RNA, while showing no detectable signal for other seasonal respiratory viruses, such as influenza. This dual-function approach underlines the versatility and potential of CRISPR technologies in both managing and detecting viral infections. Additionally, bioinformatic analysis revealed that the crRNA targets are highly conserved across animal coronaviruses, suggesting that targeting of this sequence could facilitate the rapid development of treatment options and diagnostics during a new pandemic of an emerging coronavirus. This could significantly aid in pandemic preparedness and response efforts.